Icon Disappears/Missing ?!?!

I used "Free Disk Space" to free up some space because BossTool wasn't working for some reason. I'm not sure what happened, but half of my apps are "gone". They are still in the Uninstall section of Installer which makes me think that the missing apps (including Customize, BossTool, Finder, etc) have been relocated somewhere but not linked or just not on my springboard for some reason.

I used CuteFTP and can see that the apps ON my springboard are those in /Applications. The missing ones are not there.

When I go to /private/var/Applications, i can see the missing apps. How can I either link these to my springboard or move them somewhere that I can see/use them on my iPod touch.

When I go to /private/var/root/Applications_ROOT, I can see ALL the applications on my iPod.